Background
Results
Pathogen detection
Virus isolation and identification
Sequencing results and phylogenetic analyses
Discussion
Conclusion
Materials and methods
Case description
Screening for viral pathogens
Virus isolation and identification
Sequencing and sequence analysis
Oligonucleotides | Locationa | sequence |
---|---|---|
1 F | 190-209 | GCGTTCCGTCGCCTTCTACA |
1R | 2751-2729 | CAGGAATCTGGAAGACACTTGCA |
2 F | 2663-2684 | GTATTATGCCACCAGTGTCCCA |
2R | 4957-4938 | CAGTTGCCAGCAGGCACTGT |
3 F | 4887-4906 | ACCAGCGGTGCATTGCTTGA |
3R | 7475-7453 | CAATGTGCTCTTGCAATCCTGCA |
4 F | 7327-7350 | CTGTTAAGTTAGTGGACTCAGCGT |
4R | 9875-9856 | ACTAGCGCCTTCAACTTGCA |
5 F | 9712-9731 | GCGCTTGTGGTTCACCTGGT |
5R | 12259-12240 | GGATCCACAGCGAAAGCGCA |
6 F | 12182-12202 | ACGCTTGCAGGCTGGTAAACA |
6R | 14462-14442 | TGGGCAGTGCTCTATCGCACT |
7 F | 14322-14341 | ATACTAGGGGCGCTTCGGTT |
7R | 16780-16760 | GTCAGGGTGCACAGGAATGAA |
8 F | 16662-16684 | GTATGTGTGCCCTTAAGCCTGAT |
8R | 19002-18980 | GTAAGTGGACGTTCGGCTTCATA |
9 F | 18874-18898 | CGTAGCTTTTGAGTTGTATGCCA |
9R | 21330-21309 | GCAATTAGCTGTACAGGGTTCA |
10 F | 21080-21101 | CCATTCCAGCTTATATGCGTGA |
10R | 23487-23465 | GTACATGTGAAGCTTCTCAGCGT |
11 F | 23272-23292 | GTGTACGATCCTGCAAGTGGC |
11R | 25715-25694 | TCACCTCATCAACGGGAATAGA |
12 F | 25535-25557 | TCGTCCAATTGGTTAATCTGTGC |
12R | 27840-27820 | TACCGTTGTGTGCAAGACCAA |
5’ RACE Primer | 307-288 | TTGCTAGCCATAGCCGGCAG |
3’Race Primer | 27725-27747 | CTATGTTCCAGGGTAGTGCCATT |
Strain/Isolate | Accession No, Country | Strain/Isolate | Accession No, Country |
---|---|---|---|
(a) Complete genome
| VN122M6 | HQ883484, Vietnam | |
TGEV Purdue | AJ271965, Spain | Chinju99 | DQ845249, Korea |
HCoV-229E | AF304460, Germany | KPEDV-9 | AF015888, Korea |
CV777 | AF353511, Belgium | e1697 | FJ687454, Korea |
SM98 | GU937797, Korea | BIF118 | FJ687460, Korea |
attenuated DR13 | JQ023162,Korea | CPF259 | FJ687465, Korea |
Virulent DR13 | JQ023161, Korea |
(d) N gene
| |
LZC | EF185992, China | LJB/03 | DQ072726, China |
CH/S | JN547228, China | JS-2004-2 | AY653206, China |
CH/FJND-3/2011 | JQ282909, China | S | DQ355223, China |
BJ-2011-1 | JN825712, China | CH/IMB/06 | FJ473387, China |
CHGD-01 | JX261936, China | CH/JSX/06 | FJ473388, China |
(b) S gene
| CH/HNCH/06 | FJ473389, China | |
Br1-87 | Z25483, France | CH/HLJH/06 | FJ473390, China |
NK | AB548623, Japan | CH/IMT/06 | FJ473391, China |
MK | AB548624, Japan | CH/HLJM/07 | FJ473393, China |
83P-5 | AB548618, Japan | CH/GSJ/07 | HM210880, China |
Kawahira | AB548622, Japan | CH/JL/09 | HM210881, China |
Chinju99 | AY167585, Korea | CH/GDS/09 | HM210882, China |
KNU-0801 | GU180142, Korea | CH/HLJQ/2010 | HQ455345, China |
KNU-0802 | GU180143, Korea | CH/HLJHG/2010 | HQ455346, China |
KNU-0901 | GU180144, Korea | BJ2010 | JF690780, China |
KNU-0902 | GU180145, Korea | Chinju99 | AF237764, Korea |
KNU-0903 | GU180146, Korea | 83P-5 | AB618615, Japan |
KNU-0904 | GU180147, Korea |
(e) ORF3 gene
| |
JS-2004-2 | AY653204, China | Br1/87 | Z24733, France |
DX | EU031893,China | CH/HNCH/06 | GU372738, China |
LJB-03 | DQ985739, China | CH/HLJH/06 | GU372732, China |
(c) M gene
| CH/IMT/06 | GU372739, China | |
Br1/87 | Z24733, France | CH/GSJI/07 | GU372737, China |
JS-2004-2 | AY653205, China | CH/GSJII/07 | GU372742, China |
CH/HLJH/06 | EU033964, China | CH/HLJM/07 | GU372735, China |
CH/HNCH/06 | EU033963, China | CH/JL/08 | GU372734, China |
CH/JSX/06 | EU033967, China | CH/JL/09 | GU372741, China |
YM-2007 | EU302820, China | Chinju99 | EU792474, Korea |
QH | AY974335, China | PFF285 | HQ537449, Korea |
HB/GY | JN400910, China | PFF381 | HQ537451, Korea |
HB/LF | JN400909, China | PFF513 | HQ537452, Korea |
M_NIAH380_98 | EU581712, Thailand | PFF514 | HQ537453, Korea |
M_NIAH1795_04 | EU542415, Thailand | M1763 | HQ537438, Korea |
M_NIAH2013_95 | EU581711, Thailand | BI976 | HQ537433, Korea |
VN116 M5 | HQ883483, Vietnam |